Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster

Gene duplication has been proposed to serve as the engine of evolutionary innovation. It is well recognized that eukaryotic genomes contain a large number of duplicated genes that evolve new functions or expression patterns. However, in mollusks, the evolutionary mechanisms underlying the divergence...

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Published in:Evolutionary Bioinformatics
Main Authors: Gao, Dahai, Ko, Dennis C., Tian, Xinmin, Yang, Guang, Wang, Liuyang
Format: Article in Journal/Newspaper
Language:English
Published: SAGE Publications 2015
Subjects:
Online Access:http://dx.doi.org/10.4137/ebo.s30230
http://journals.sagepub.com/doi/pdf/10.4137/EBO.S30230
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spelling crsagepubl:10.4137/ebo.s30230 2023-05-15T17:54:16+02:00 Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster Gao, Dahai Ko, Dennis C. Tian, Xinmin Yang, Guang Wang, Liuyang 2015 http://dx.doi.org/10.4137/ebo.s30230 http://journals.sagepub.com/doi/pdf/10.4137/EBO.S30230 http://journals.sagepub.com/doi/full-xml/10.4137/EBO.S30230 en eng SAGE Publications http://journals.sagepub.com/page/policies/text-and-data-mining-license Evolutionary Bioinformatics volume 11s1, page EBO.S30230 ISSN 1176-9343 1176-9343 Computer Science Applications Genetics Ecology, Evolution, Behavior and Systematics journal-article 2015 crsagepubl https://doi.org/10.4137/ebo.s30230 2022-04-14T04:35:46Z Gene duplication has been proposed to serve as the engine of evolutionary innovation. It is well recognized that eukaryotic genomes contain a large number of duplicated genes that evolve new functions or expression patterns. However, in mollusks, the evolutionary mechanisms underlying the divergence and the functional maintenance of duplicate genes remain little understood. In the present study, we performed a comprehensive analysis of duplicate genes in the protein kinase superfamily using whole genome and transcriptome data for the Pacific oyster. A total of 64 duplicated gene pairs were identified based on a phylogenetic approach and the reciprocal best BLAST method. By analyzing gene expression from RNA-seq data from 69 different developmental and stimuli-induced conditions (nine tissues, 38 developmental stages, eight dry treatments, seven heat treatments, and seven salty treatments), we found that expression patterns were significantly correlated for a number of duplicate gene pairs, suggesting the conservation of regulatory mechanisms following divergence. Our analysis also identified a subset of duplicate gene pairs with very high expression divergence, indicating that these gene pairs may have been subjected to transcriptional subfunctionalization or neofunctionalization after the initial duplication events. Further analysis revealed a significant correlation between expression and sequence divergence (as revealed by synonymous or nonsynonymous substitution rates) under certain conditions. Taken together, these results provide evidence for duplicate gene sequence and expression divergence in the Pacific oyster, accompanying its adaptation to harsh environments. Our results provide new insights into the evolution of duplicate genes and their expression levels in the Pacific oyster. Article in Journal/Newspaper Pacific oyster SAGE Publications (via Crossref) Pacific Evolutionary Bioinformatics 11s1 EBO.S30230
institution Open Polar
collection SAGE Publications (via Crossref)
op_collection_id crsagepubl
language English
topic Computer Science Applications
Genetics
Ecology, Evolution, Behavior and Systematics
spellingShingle Computer Science Applications
Genetics
Ecology, Evolution, Behavior and Systematics
Gao, Dahai
Ko, Dennis C.
Tian, Xinmin
Yang, Guang
Wang, Liuyang
Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster
topic_facet Computer Science Applications
Genetics
Ecology, Evolution, Behavior and Systematics
description Gene duplication has been proposed to serve as the engine of evolutionary innovation. It is well recognized that eukaryotic genomes contain a large number of duplicated genes that evolve new functions or expression patterns. However, in mollusks, the evolutionary mechanisms underlying the divergence and the functional maintenance of duplicate genes remain little understood. In the present study, we performed a comprehensive analysis of duplicate genes in the protein kinase superfamily using whole genome and transcriptome data for the Pacific oyster. A total of 64 duplicated gene pairs were identified based on a phylogenetic approach and the reciprocal best BLAST method. By analyzing gene expression from RNA-seq data from 69 different developmental and stimuli-induced conditions (nine tissues, 38 developmental stages, eight dry treatments, seven heat treatments, and seven salty treatments), we found that expression patterns were significantly correlated for a number of duplicate gene pairs, suggesting the conservation of regulatory mechanisms following divergence. Our analysis also identified a subset of duplicate gene pairs with very high expression divergence, indicating that these gene pairs may have been subjected to transcriptional subfunctionalization or neofunctionalization after the initial duplication events. Further analysis revealed a significant correlation between expression and sequence divergence (as revealed by synonymous or nonsynonymous substitution rates) under certain conditions. Taken together, these results provide evidence for duplicate gene sequence and expression divergence in the Pacific oyster, accompanying its adaptation to harsh environments. Our results provide new insights into the evolution of duplicate genes and their expression levels in the Pacific oyster.
format Article in Journal/Newspaper
author Gao, Dahai
Ko, Dennis C.
Tian, Xinmin
Yang, Guang
Wang, Liuyang
author_facet Gao, Dahai
Ko, Dennis C.
Tian, Xinmin
Yang, Guang
Wang, Liuyang
author_sort Gao, Dahai
title Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster
title_short Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster
title_full Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster
title_fullStr Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster
title_full_unstemmed Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster
title_sort expression divergence of duplicate genes in the protein kinase superfamily in pacific oyster
publisher SAGE Publications
publishDate 2015
url http://dx.doi.org/10.4137/ebo.s30230
http://journals.sagepub.com/doi/pdf/10.4137/EBO.S30230
http://journals.sagepub.com/doi/full-xml/10.4137/EBO.S30230
geographic Pacific
geographic_facet Pacific
genre Pacific oyster
genre_facet Pacific oyster
op_source Evolutionary Bioinformatics
volume 11s1, page EBO.S30230
ISSN 1176-9343 1176-9343
op_rights http://journals.sagepub.com/page/policies/text-and-data-mining-license
op_doi https://doi.org/10.4137/ebo.s30230
container_title Evolutionary Bioinformatics
container_volume 11s1
container_start_page EBO.S30230
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